Hi Peng, there's a lot going on there, and it is not specific enough for me to make recommendations. Take a look at the docs we have on our coordinate systems
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.pdf you might get the answer you need from there or at least use our terminology to point me in the right direction doug On 03/10/2014 12:20 PM, peng wrote: > Thanks Doug for your reply. In fact I need both. I do this mainly for > computation (in volume); and display (in surface) is also cool. > > The dots (e.g. A1, A2, ..., An, ..., AN) were originally defined in > volume of the template (icbm152). This can be implemented as an Nx3 > matrix S, where S(n, :) = [nx, ny, nz] indicates the location of An in > the volume. > RAS here I mean such a coordinate system that, [0 0 0] is AC and the 3 > dimensions are taking right, anterior, superior as positive, e.g > An([nx0 ny0 nz0]) indicates a location nx0 mm right, ny0 mm anterior > and nz0 mm superior of AC. > The above two systems can be easily transformed by a transformation > matrix. > > I wish to know the correspondent locations of An in individual > subject(B), as Bn. e.g. if A1 is center of V1 in the template, I wish > to find the center of V1 in the subject as B1. > So far, all the locations are represented in volume. However, I guess > to normalise the individual brain to the template, freesurfer will > extract the volumes to surfaces. I imagine the procedure will be like > An (volume representation of dots in template) -> ASn (surface > representation of dots in template) -> BSn(surface representation of > dots in individual) -> Bn(volume representation of dots in > individual). If this assumption is correct, I would like to use Bn for > my computation and ASn for display later. > > I hope I have made myself clearer. > > best > Peng > > > On Mon, Mar 10, 2014 at 4:21 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > Do you mean you want to display them in the MRI volume or on the > surface > (or both)? When you say that they are in "RAS coordinates", what > do you > mean? How are the coords defined? > doug > > > > On 03/08/2014 07:26 AM, peng wrote: > > Dear freesurfers, > > > > I have a set of dot locations (300~400) in a template brain, > > indicated by indices of a 3-D array of the template MRI data, which > > can be easily transformed to RAS coordinates. I wish to project > these > > dot locations to individual MRIs, ideally also as indicated by > indices > > in the 3-D array of the individual MRI data. Is it possible to do it > > in freesurfer? I guess the surface-based procedure shall work > well for > > this. It might be a very junior question, if it was documented > > somewhere before, please let me know the link. Thank you very > much for > > help. > > > > best > > Peng > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
